High-throughput analysis of adaptation using barcoded strains of Saccharomyces cerevisiae
release_256xzzhph5eonllgirzp2c2nvu
by
Vincent J. Fasanello, Ping Liu, Carlos A. Botero, Justin C. Fay
Abstract
<jats:sec>
<jats:title>Background</jats:title>
Experimental evolution of microbes can be used to empirically address a wide range of questions about evolution and is increasingly employed to study complex phenomena ranging from genetic evolution to evolutionary rescue. Regardless of experimental aims, fitness assays are a central component of this type of research, and low-throughput often limits the scope and complexity of experimental evolution studies. We created an experimental evolution system in <jats:italic>Saccharomyces cerevisiae</jats:italic> that utilizes genetic barcoding to overcome this challenge.
</jats:sec>
<jats:sec>
<jats:title>Results</jats:title>
We first confirm that barcode insertions do not alter fitness and that barcode sequencing can be used to efficiently detect fitness differences via pooled competition-based fitness assays. Next, we examine the effects of ploidy, chemical stress, and population bottleneck size on the evolutionary dynamics and fitness gains (adaptation) in a total of 76 experimentally evolving, asexual populations by conducting 1,216 fitness assays and analyzing 532 longitudinal-evolutionary samples collected from the evolving populations. In our analysis of these data we describe the strengths of this experimental evolution system and explore sources of error in our measurements of fitness and evolutionary dynamics.
</jats:sec>
<jats:sec>
<jats:title>Conclusions</jats:title>
Our experimental treatments generated distinct fitness effects and evolutionary dynamics, respectively quantified via multiplexed fitness assays and barcode lineage tracking. These findings demonstrate the utility of this new resource for designing and improving high-throughput studies of experimental evolution. The approach described here provides a framework for future studies employing experimental designs that require high-throughput multiplexed fitness measurements.
</jats:sec>
In application/xml+jats
format
Archived Files and Locations
application/pdf 337.7 kB
file_hmfmwbldg5bkjgd242dddzpmaa
|
peerj.com (publisher) web.archive.org (webarchive) |
Open Access Publication
In DOAJ
In ISSN ROAD
In Keepers Registry
ISSN-L:
2167-8359
access all versions, variants, and formats of this works (eg, pre-prints)
Crossref Metadata (via API)
Worldcat
SHERPA/RoMEO (journal policies)
wikidata.org
CORE.ac.uk
Semantic Scholar
Google Scholar